The microcrustacean Daphnia, commonly referred to as the water flea, has been subject to intense biological investigations for over a century. The development of genomic infrastructure coupled with a wide range of phenotypic diversity make Daphnia a versatile model system to investigate fundamental mechanisms of inheritance and development, cellular function, physiological systems, immunity response, disease, macromolecular structure/function relationships, and the genetic basis of complex phenotypic traits. Daphnia has a rich literature documenting its ecological diversity making it an ideal model for investigating the genetic architecture underlying phenotypic variation in natural populations. Daphnia is a sensitive sentinel species in freshwater ecosystems and is widely used as a model for ecotoxicological studies. Increasingly, Daphnia is used as a surrogate species to understand genomic responses to environmental stressors that are important factors in human health and well being.
Characteristics and Advantages
- A complete draft assembly of the D. pulex genome is available through collaboration of the U.S. DoE’s Joint Genome Institute and the Daphnia Genomics Consortium (DGC) (http://genome.jgi-psf.org/Dappu1/Dappu1.home.html). The sequence coverage using the whole genome shotgun method is 8.72x ± 0.10 fold. In total, the size of the euchromatic portion of the genome is estimated to be 200-227 Mb. The genome sequence is supported by an international research community actively building additional resources for its annotation and functional characterization.
- The phylogenetic position of Daphnia is ideal for comparative genomics. The number of model systems available for understanding genome function and evolution is rapidly expanding. This rapid growth is particularly noticeable in insect taxa. The close relationship of the crustacea and insects is clearly supported by both molecular and morphological studies making Daphnia a valuable outgroup for comparative genomic studies.
- Genomic resources include genomic & cDNA libraries, microarrays, tiling arrays, genetic linkage maps, web-based bioinformatics portal, annotation and gene expression databases, and a well-resolved phylogenetic framework throughout the genus Daphnia.
- The reproductive cycle of Daphnia is ideal for experimental genetics. Generation time in the lab rivals that of almost all other model eukaryotic systems. Daphnia are easily cultured and reach maturity within 5 - 10 days. Reproduction is normally clonal (allowing the maintenance of genetic lineages), but sex can be induced environmentally (allowing the production of inbred or outbred lineages). The clonal nature of the organism provides an exceptional opportunity to study genetic responses to environmental stimuli in a defined and constant genetic background with unlimited replication. Daphnia are an exceptional model for studying developmental and disease processes. Daphnia are transparent throughout lifeallowing for studies of tissue-specific gene expression at any life stage and direct observation of parasites and pathogens.
- Daphnia have a wide, nearly cosmopolitan, distribution. They occur in a highly diverse set of habitats ranging from freshwater lakes to saline ponds. As a result they manifest extensive phenotypic diversity providing ample raw material to study gene function and genome by environment interactions.